Press Release
Media Contact:
Singapore: sec@apbionet.org
CRAY INC., LION BIOSCIENCE, KOOPRIME and APBIONET ENGINEERS
PROVIDE A RECIPE FOR BIOINFORMATICS:
WORKING TOWARDS AN INTEGRATED DATA-COMPUTE-WORKFLOW PLATFORM
SINGAPORE, June 20, 2002. The Asia Pacific Bioinformatics Network (APBioNet) which promotes the growth of Bioinformatics in the Asia Pacific region, has identified one of the biggest obstacles to widespread adoption amongst life scientists as the lack of integration and interoperability amongst the disparate bioinformatics software vendors, database providers and instrument devices.
In setting up a testbed pilot project, APBioNet is pleased to announce that it is currently working with the best of breed bioinformatics database provider Lion BioScience (Neuer Markt: LIO, WKN 504 350; Nasdaq: LEON) to integrate their popular SRS system with supercomputing pioneer Cray Inc (Nasdaq NM: CRAY) through the use of KOOPrime's applications integration system.
Said Dr Tin Wee Tan, APBioNet secretariat and co-founder, "Our bioinformatics user community has moved from command-line interfaces to nice but tedious GUIs, to repetitive Web form-filling and back. What we need is a protocol-based recipe system which biologists are familiar with, that allows us to stitch together things we do repeatedly, and to schedule and automate the workflow processes we have to grapple with daily."
KOOPrime's applications integration system allows users to integrate data handling and instrument control from laboratory devices with database access and computational analysis. Until now, the database component and compute integration has been on an ad hoc basis, and restricted to an enterprise-wide framework.
By combining technologies from KooPrime, Lion BioScience and Cray Inc and operating an Internet-wide bioinformatics workflow applications integration testbed, APBioNet aims to pioneer the concept of privately reusable, publicly contributed workflows and objects that can facilitate the seamless flow of data from devices to databases and computation servers across the Internet. This will help ease the problem with the integration of non-interoperable systems.
Said the Chief Architect of Lion BioScience's SRS Dr Thure Etzold: "We are pleased to cooperate with APBioNet, and will work towards unleashing the comprehensive spectrum of biological databases our ubiquitous SRS system provides, into the workflows which every bioinformaticist currently carries out either manually or through time-consuming scripting."
"Automated device data gathering and complex database operations are incomplete without high performance compute power. Cray Inc has previously worked with the APBioNet to launch a BioCray grid computing network and with the National University of Singapore to build Cray Bioinformatics Libraries," said Dick Russell, Vice President of Cray Inc. "We now want to have that deeper integration with the biologist's workflow which includes data acquisition, database searching, and computation. Our role is to make the computational time transparent to the user so that they don't have to worry about it."
Describing how the integration works, KOOPrime's CEO, T.S. Lim explains, "We provide the platform for treating each step of a complex series of activities a biologist or bioinformaticist carries out as a "bubble". By linking the output of one bubble to the input of the next bubble in a user-friendly manner, we can assemble complex workflows of bubbles and links."
In this collaboration, KOOP bubbles are now built to wrap around SRS databases and the computational biology applications running on Cray supercomputers that are part of Computational Grids like APBioGrid. "We are pleased that APBioNet is extending our enterprise system across the Internet," Lim added, "And it will allow participating users to write their bubbles and share their workflows with each other."
"My biggest challenge is probably how to get people to build workflows, and share them with each other." said Dr Tan, who conceived the idea and is currently coordinating the whole project. "We already have a set of more than 200 bubbles, including 160 from the EMBOSS suite, 40 from PHYLIP, 20 Unix utilities, a dozen from MySQL, a few for Globus Grid, BLAST, FASTA and CLUSTALW. Linking up with Cray Inc and Lion Bioscience will help increase the power of this new workflow paradigm. It will shift the one-biologist one-workbench thought pattern to that of virtual Internet-wide, automated, shareable and reusable processes."
About LION Bioscience AG:
(Neuer Markt: LIO, WKN 504 350; Nasdaq: LEON)
LION Bioscience provides proven information and knowledge
management solutions to significantly improve life science R&D
performance and productivity. These solutions integrate all R&D
disciplines, spanning from genomics to early and late discovery through
clinical trials. LION applies these solutions for its internal drug
discovery program in the field of nuclear receptors with the goal to
out-license specific databases, polymorphism marker panels, and
validated targets and leads. Founded in 1997, LION has more than
485 employees, with headquarters in Heidelberg, Germany, and subsidiaries
in Cambridge, UK, Cambridge, MA, USA and San Diego, CA, USA.
To date, LION has established partnerships with leading life science
companies, including Aventis, Bayer, Boehringer Ingelheim, Celera,
DuPont, GlaxoSmithKline, Janssen, Merck Inc., Nestlé, Novartis,
Paradigm Genetics, Pharmacia & Upjohn, Roche, Sumitomo Pharmaceuticals
and Tripos. Please see www.lionbioscience.com for more information.
About Cray Inc:
(NASDAQ NM: CRAY)
Cray is the premier provider of supercomputing solutions for
customers' most challenging scientific and engineering problems. Go to
www.cray.com for more information about the company.
Go to http://www.cray.com/
for more information about the company.
About KOOPrime:
KOOPrime Pte Ltd is one of the first software companies providing
Enterprise Application Integration services and products to the
life sciences industry. Founded in 2000 as a spin-off company
from the National University of Singapore, the company focuses on
allowing seamless and transparent flow of data and information from
one component to another, resulting in business flows that can be
visually personalized and automated by end users themselves.
These technologies have been applied in High Throughput Screening
for Drug Discovery, Microarray Fabrication and Analysis for
Functional Genomics, Web Application Integration for content and
functional integration of Bioinformatics websites and databases.
KOOPrime aims to provide one-stop IT solutions to existing and
up-and-coming life science organizations. With its extended reach
to work with partners in the Asian, US and European regions,
KOOPrime is able to address IT needs in the life sciences effectively.
For more information, please refer to www.kooprime.com.
About APBioNet:
The Asia Pacific Bioinformatics Network (APBioNet) is a non-profit,
non-governmental, international organization founded in 1998. It focuses
on the promotion of bioinformatics in the Asia Pacific Region. Since 1998,
its mission has been to pioneer the growth and development of
bioinformatics awareness, training, education, infrastructure, resources
and research amongst member countries and economies. Its work includes the
technical coordination, liaison and/or affiliation with other
international bodies such as the EMBnet and ISCB.
APBioNet has more than 20 organizational and 400 individual members from
over 12 countries in the Asia Pacific region. It is spearheading a number
of key bioinformatics initiatives in the region in collaboration with
international organizations such as APAN, APEC, S* Alliance and A-IMBN
and with industry partners. More about
APBioNet can be found at: http://www.apbionet.org/.
Media Contacts:
Cray Inc
Contact: Steve Conway
Tel: +651-592-7441
Email: sttico@aol.com
Cray Singapore
Raj Godhia
Tel: +65-63559356
Email: godhia@cray.com
LION bioscience AG:
Europe: Dr. Andrea Kreisselmeier.
Telephone +49 (0)6221-4038-265,
Email andrea.kreisselmeier@lionbioscience.com
KooPrime Pte Ltd
Asia: Anwar Chan
Tel: +65-98453370
Email: anwar@kooprime.com
APBioNet Secretariat
Dr Tan Tin Wee
Tel: +65-9664-0347
Email: sec@apbionet.org